A database for G proteins and their interaction with GPCRs

Background

The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development.

Results

BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database http://www.hprd.org, a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange.

Conclusions

As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL.     

Identification of the hepatitis C virus E2 glycoprotein binding site on the large extracellular loop of CD81

The binding of hepatitis C virus glycoprotein E2 to the large extracellular loop (LEL) of CD81 has been shown to modulate human T-cell and NK cell activity in vitro. Using random mutagenesis of a chimera of maltose-binding protein and LEL residues 113 to 201, we have determined that the E2-binding site on CD81 comprises residues Ile(182), Phe(186), Asn(184), and Leu(162). These findings reveal an E2-binding surface of approximately 806 A(2) and potential target sites for the development of small-molecule inhibitors of E2 binding.     

Describing the Breakbone Fever: IDODEN,an Ontology for Dengue Fever

Background

Ontologies represent powerful tools in information technology because they enhance interoperability and facilitate, among other things, the construction of optimized search engines. To address the need to expand the toolbox available for the control and prevention of vector-borne diseases we embarked on the construction of specific ontologies. We present here IDODEN, an ontology that describes dengue fever, one of the globally most important diseases that are transmitted by mosquitoes.

Methodology/Principal Findings

We constructed IDODEN using open source software, and modeled it on IDOMAL, the malaria ontology developed previously. IDODEN covers all aspects of dengue fever, such as disease biology, epidemiology and clinical features. Moreover, it covers all facets of dengue entomology. IDODEN, which is freely available, can now be used for the annotation of dengue-related data and, in addition to its use for modeling, it can be utilized for the construction of other dedicated IT tools such as decision support systems.

Conclusions/Significance

The availability of the dengue ontology will enable databases hosting dengue-associated data and decision-support systems for that disease to perform most efficiently and to link their own data to those stored in other independent repositories, in an architecture- and software-independent manner.     

Risk factors for fouling biomass: evidence from small vessels in Australia

Abstract

Invasive non-indigenous species (NIS) are a threat to marine biodiversity and marine reliant industries. Recreational vessels are recognised as an important vector of NIS translocation, particularly domestically. This paper reports on a novel application of multilevel modelling and multiple imputation in order to quantify the relationship between biofouling biomass (wet weight) and the vessel-level characteristics of recreational and fishing vessels. It was found that the number of days since the vessel was last cleaned strongly related to the biofouling biomass, yet differed dependent on vessel type. Similarly, the median number of trips undertaken was related to the biofouling biomass, and varied according to the type of antifouling paint (AF) used. No relationship was found between vessel size and biofouling biomass per sample unit. To reduce the spread of NIS, vessel owners should use an AF paint suitable to their vessel’s operational profile, and follow a maintenance schedule according to the paint manufacturer’s specifications.     

Trophoblast-specific gene manipulation using lentivirus-based vectors

The trophoblast layers of the mammalian placenta carry out many complex functions required to pattern the developing embryo and maintain its growth and survival in the uterine environment. Genetic disruption of many gene pathways can result in embryonic lethality because of placental failure, potentially confusing the interpretation of mouse knockout phenotypes. Development of tools to specifically and efficiently manipulate gene expression in the trophoblast lineage would greatly aid understanding of the relative roles of different genetic pathways in the trophoblast versus embryonic lineages. We show that short-term lentivirus-mediated infection of mouse blastocysts can lead to rapid expression of a green fluorescent protein (GFP) transgene specifically in the outer trophoblast progenitors and their later placental derivatives. Efficient trophoblast-specific gene knockdown can also be produced by lentivirus-mediated pol III-driven short hairpin RNA (shRNA) and efficient trophoblast-specific gene knockout by pol II-driven Cre recombinase lentiviral vectors. This lentivirus lineage-specific infection system thus facilitates both gain and loss of function studies during placental development in the mouse and potentially other mammalian species.     

Prediction of cell wall sorting signals in gram-positive bacteria with a hidden markov model: application to complete genomes

Surface proteins in Gram-positive bacteria are frequently implicated in virulence. We have focused on a group of extracellular cell wall-attached proteins (CWPs), containing an LPXTG motif for cleavage and covalent coupling to peptidoglycan by sortase enzymes. A hidden Markov model (HMM) approach for predicting the LPXTG-anchored cell wall proteins of Gram-positive bacteria was developed and compared against existing methods. The HMM model is parsimonious in terms of the number of freely estimated parameters, and it has proved to be very sensitive and specific in a training set of 55 experimentally verified LPXTG-anchored cell wall proteins as well as in reliable data sets of globular and transmembrane proteins. In order to identify such proteins in Gram-positive bacteria, a comprehensive analysis of 94 completely sequenced genomes has been performed. We identified, in total, 860 LPXTG-anchored cell wall proteins, a number that is significantly higher compared to those obtained by other available methods. Of these proteins, 237 are hypothetical proteins according to the annotation of SwissProt, and 88 had no homologs in the SwissProt database--this might be evidence that they are members of newly identified families of CWPs. The prediction tool, the database with the proteins identified in the genomes, and supplementary material are available online at http://bioinformatics.biol.uoa.gr/CW-PRED/.     

The level of hypotension during hemorrhagic shock is a major determinant of the post-resuscitation systemic inflammatory response: an experimental study

Background

To evaluate whether the level of hypotension during hemorrhagic shock may influence the oxidative and inflammatory responses developed during post-ischemic resuscitation.

Methods

Fifteen rabbits were equally allocated into three groups: sham-operated (group sham); bled within 30 minutes to mean arterial pressure (MAP) of 40 mmHg (group shock-40); bled within 30 minutes to MAP of 30 mmHg (group shock-30). Shock was maintained for 60 min. Resuscitation was performed by reinfusing shed blood with two volumes of Ringer's lactate and blood was sampled for estimation of serum levels aminotransferases, creatinine, TNF-α, IL-1β, IL-6, malondialdehyde (MDA) and total antioxidant status (TAS) and for the determination of oxidative burst of polymorhonuclears (PMNs) and mononuclear cells (MCs).

Results

Serum AST of group shock-30 was higher than that of group shock-40 at 60 and 120 minutes after start of resuscitation; serum creatinine of group shock-30 was higher than group shock-40 at 120 minutes. Measured cytokines, MDA and cellular oxidative burst of groups, shock-40 and shock-30 were higher than group sham within the first 60 minutes after start of resuscitation. Serum concentrations of IL-1β, IL-6 and TNF-α of group shock-30 were higher than group shock-40 at 120 minutes (p < 0.05). No differences were found between two groups regarding serum MDA and TAS and oxidative burst on PMNs and MCs but both groups were different to group sham.

Conclusion

The level of hypotension is a major determinant of the severity of hepatic and renal dysfunction and of the inflammatory response arising during post-ischemic hemorrhagic shock resuscitation. These findings deserve further evaluation in the clinical setting.     

A unification of multivariate methods for meta-analysis of genetic association studies

Methods for multivariate meta-analysis of genetic association studies are reviewed, summarized and presented in a unified framework. Modifications of standard models are described in detail in order to be applied in genetic association studies. The model based on summary data is uniformly defined for both discrete and continuous outcomes and analytical expressions for the covariance of the two jointly modeled outcomes are derived for both cases. The models based on the binary nature of the data are fitted using both prospective and retrospective likelihood. Furthermore, formal tests for assessing the genetic model of inheritance are developed based on standard normal theory. The general model is compared to the recently proposed genetic model-free bivariate approach (either using summary or binary data), and it is clearly shown that the estimates provided by this approach are nearly identical to the estimates derived by the general bivariate model using the aforementioned tests for the genetic model. The methods developed here as well as the tests, are easily implemented in all major statistical packages, escaping the need of self written software. The methods are applied in several already published meta-analyses of genetic association studies (with both discrete and continuous outcomes) and the results are compared against the widely used univariate approach as well as against the genetic model free approaches. Illustrative examples of code in Stata are given in the appendix. It is anticipated that the methods developed in this work will be widely applied in the meta-analysis of genetic association studies.